incendilabs · kennethmyhra · Feb 9, 2025 · Feb 8, 2025 · Feb 9, 2025 · Feb 9, 2025
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -0,0 +1,71 @@
+name: CI
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - 'master'
+  pull_request:
+
+jobs:
+  build:
+    if: github.repository == 'incendilabs/plan-executor'
+
+    runs-on: ubuntu-24.04
+    steps:
+      -
+        name: Checkout repo
+        uses: actions/checkout@v4
+      -
+        name: Build docker image
+        run: docker build -t incendi/plan_executor:latest .
+      -
+        name: Run tests
+        run: |
+          mkdir -p logs html_summaries json_results
+          docker compose up -d spark
+          docker compose run --rm --no-deps plan_executor ./execute_all.sh 'http://spark:8080/fhir' r4 'html|json|stdout'
+          docker compose logs spark > logs/backend.log
+      -
+        name: Combine test results
+        if: ${{ always() }}
+        run: ./combine-test-results.sh json_results annotations.json
+      -
+        name: Attach test results
+        if: github.event_name != 'pull_request'
+        uses: yuzutech/annotations-action@v0.5.0
+        with:
+          repo-token: "${{ secrets.GITHUB_TOKEN }}"
+          input: annotations.json
+      -
+        name: Archive logs
+        if: ${{ always() }}
+        uses: actions/upload-artifact@v4
+        with:
+          name: logs-r4-${{ github.sha }}
+          path: logs/*.log*
+      -
+        name: Archive test reports
+        if: ${{ always() }}
+        uses: actions/upload-artifact@v4
+        with:
+          name: html_summaries-r4-${{ github.sha }}
+          path: html_summaries/**/*.html
+      -
+        name: Archive JSON results
+        if: ${{ always() }}
+        uses: actions/upload-artifact@v4
+        with:
+          name: json_results-r4-${{ github.sha }}
+          path: json_results/**/*.json
+      -
+        name: Archive annotations file
+        if: ${{ always() }}
+        uses: actions/upload-artifact@v4
+        with:
+          name: annotations-r4-${{ github.sha }}
+          path: annotations.json
+      -
+        name: Cleanup
+        if: ${{ always() }}
+        run: docker compose down
diff --git a/Dockerfile b/Dockerfile
@@ -1,8 +1,8 @@
-FROM ruby:3.0.7
+FROM ruby:3.2.7
 
 WORKDIR /app
 COPY . ./
-RUN gem install bundler -v 2.5.13
+RUN gem install bundler -v 2.4.19
 RUN bundle install
 
-ENTRYPOINT []
+ENTRYPOINT []
diff --git a/Gemfile.lock b/Gemfile.lock
@@ -60,7 +60,7 @@ GEM
     addressable (2.7.0)
       public_suffix (>= 2.0.2, < 5.0)
     ansi (1.5.0)
-    awesome_print (1.8.0)
+    awesome_print (1.9.2)
     bcp47 (0.3.3)
       i18n
     coderay (1.1.3)
@@ -94,16 +94,15 @@ GEM
     mime-types (3.3.1)
       mime-types-data (~> 3.2015)
     mime-types-data (3.2020.1104)
-    mini_portile2 (2.4.0)
+    mini_portile2 (2.8.8)
     minitest (5.14.4)
     multi_json (1.15.0)
     multi_xml (0.6.0)
     multipart-post (2.1.1)
     netrc (0.11.0)
-    nokogiri (1.10.10)
-      mini_portile2 (~> 2.4.0)
-    nokogiri (1.10.10-x64-mingw32)
-      mini_portile2 (~> 2.4.0)
+    nokogiri (1.18.2)
+      mini_portile2 (~> 2.8.2)
+      racc (~> 1.4)
     nokogiri-diff (0.2.0)
       nokogiri (~> 1.5)
       tdiff (~> 0.3, >= 0.3.2)
@@ -114,14 +113,16 @@ GEM
       multi_xml (~> 0.5)
       rack (>= 1.2, < 3)
     power_assert (1.2.0)
-    pry (0.13.1)
+    pry (0.15.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    pry-coolline (0.2.5)
+    pry-coolline (0.2.6)
       coolline (~> 0.5)
+      pry (~> 0.13)
     public_suffix (4.0.6)
+    racc (1.8.1)
     rack (2.2.3)
-    rake (13.0.1)
+    rake (13.2.1)
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
       http-cookie (>= 1.0.2, < 2.0)
@@ -134,17 +135,17 @@ GEM
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
     ruby2_keywords (0.0.2)
-    simplecov (0.20.0)
+    simplecov (0.22.0)
       docile (~> 1.1)
       simplecov-html (~> 0.11)
       simplecov_json_formatter (~> 0.1)
     simplecov-html (0.12.3)
     simplecov_json_formatter (0.1.2)
     tdiff (0.3.4)
-    test-unit (3.3.7)
+    test-unit (3.6.7)
       power_assert
     thread_safe (0.3.6)
-    tilt (2.0.10)
+    tilt (2.6.0)
     tzinfo (1.2.8)
       thread_safe (~> 0.1)
     tzinfo-data (1.2020.4)
@@ -154,7 +155,7 @@ GEM
     unf_ext (0.0.7.7)
     unf_ext (0.0.7.7-x64-mingw32)
     unicode_utils (1.4.0)
-    webmock (3.10.0)
+    webmock (3.13.0)
       addressable (>= 2.3.6)
       crack (>= 0.3.2)
       hashdiff (>= 0.4.0, < 2.0.0)
@@ -180,4 +181,4 @@ DEPENDENCIES
   webmock
 
 BUNDLED WITH
-   2.2.17
+   2.4.19
diff --git a/combine-test-results.sh b/combine-test-results.sh
@@ -0,0 +1,58 @@
+#!/bin/bash
+
+set -e
+
+JSON_PATH=$1
+ANNOTATIONS_FILE=$2
+
+function usage() {
+  me=`basename "$0"`
+  if [ ! -z "$1" ]; then
+    echo $1
+  fi
+  echo "Usage: ./${me} path/to/input/json_results path/to/output/annotations.json"
+  exit 1
+}
+
+[ $# -eq 2 ] || usage
+
+[ ! -z "${JSON_PATH}" ] || usage
+
+[ -d "${JSON_PATH}" ] || usage "${JSON_PATH} must be a directory"
+
+touch $ANNOTATIONS_FILE || "$ANNOTATIONS_FILE is not writable"
+
+DIR=$(pwd)
+
+cd ${JSON_PATH}
+
+# Output summary to stdout
+
+ls _summary*.json | xargs jq -r '. | "PASS: \(.pass // 0)
+FAIL: \(.fail // 0)
+ERROR: \(.error // 0)
+SKIP: \(.skip // 0)"
+'
+
+# Have to use warning annotation level, notice isn't working anymore (but could be in future).
+
+SUMMARY=$(ls _summary*.json | xargs jq '[ .
+  | { "file": ".github/workflow/integration_tests.yml",  "line": 1, "message": ("PASS: \(.pass // 0)\nFAIL: \(.fail // 0)\nERROR: \(.error // 0)\nSKIP: \(.skip // 0)"), "annotation_level": "warning" }
+]')
+
+FAILURES=$(ls -I '_summary*.json' | xargs -I '{}' jq '[ .[]
+    | select(((.status == "skip") and (.message | contains("TODO") | not))
+        or .status == "fail"
+        or .status == "error")
+    | .id as $id
+    | .status as $status
+    | .message as $message
+    | .description as $description
+    | .test_method as $method
+    | input_filename as $file
+    | { "file": ".github/workflow/integration_tests.yml",  "line": 1, "message": ($id + ": " + $message), "annotation_level": "failure" }
+]' '{}')
+
+cd $DIR
+
+jq 'reduce inputs as $i (.; . += $i)' <(echo "${SUMMARY}") <(echo "${FAILURES}") > ${ANNOTATIONS_FILE}
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -0,0 +1,32 @@
+services:
+  spark:
+    container_name: spark
+    restart: always
+    image: sparkfhir/spark:r4-latest
+    environment:
+      - StoreSettings__ConnectionString=mongodb://root:secret@mongodb:27017/spark?authSource=admin
+      - SparkSettings__Endpoint=http://spark:8080/fhir
+      - ASPNETCORE_URLS=http://+:8080
+      - ASPNETCORE_HTTP_PORT=8080
+    ports:
+      - "8000:8080"
+      - "8001:8081"
+    depends_on:
+      - mongodb
+  mongodb:
+    container_name: mongodb
+    image: sparkfhir/mongo:r4-latest
+    environment:
+      MONGO_INITDB_ROOT_USERNAME: root
+      MONGO_INITDB_ROOT_PASSWORD: secret
+    ports:
+      - "17017:27017"
+  plan_executor:
+    container_name: plan_executor
+    image: incendi/plan_executor:latest
+    depends_on:
+      - spark
+    volumes:
+      - ./logs:/app/logs:rw
+      - ./html_summaries:/app/html_summaries:rw
+      - ./json_results:/app/json_results:rw
diff --git a/lib/data/resources.rb b/lib/data/resources.rb
@@ -251,7 +251,7 @@ def load_fixture(path, extension)
 
       # FIXME: Determine a better way to share fixture data with Crucible
       def fixture_path
-        if File.exists?(FIXTURE_DIR)
+        if File.exist?(FIXTURE_DIR)
           FIXTURE_DIR
         else
           File.join(Rails.root, 'test', 'fixtures')